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JMassBalance: mass-balanced randomization and analysis of metabolic networks

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http://pubman.mpdl.mpg.de/cone/persons/resource/persons97064

Basler,  G.
Mathematical Modelling and Systems Biology - Nikoloski, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97320

Nikoloski,  Z.
Mathematical Modelling and Systems Biology - Nikoloski, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Basler, G., & Nikoloski, Z. (2011). JMassBalance: mass-balanced randomization and analysis of metabolic networks. Bioinformatics, 27(19), 2761-2762. doi:10.1093/bioinformatics/btr448.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0014-226A-4
Abstract
Analysis of biological networks requires assessing the statistical significance of network-based predictions by using a realistic null model. However, the existing network null model, switch randomization, is unsuitable for metabolic networks, as it does not include physical constraints and generates unrealistic reactions. We present JMassBalance, a tool for mass-balanced randomization and analysis of metabolic networks. The tool allows efficient generation of large sets of randomized networks under the physical constraint of mass balance. In addition, various structural properties of the original and randomized networks can be calculated, facilitating the identification of the salient properties of metabolic networks with a biologically meaningful null model.